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annotate dnabot.xml @ 0:6d55c77a17ab draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Tue, 14 Dec 2021 16:13:36 +0000
parents
children de6812daba39
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1 <tool id="dnabot" name="DNA-Bot" version="3.0.0">
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2 <description>DNA assembly using BASIC on OpenTrons</description>
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3 <requirements>
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4 <requirement type="package" version="3.0.0">dnabot</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python -m dnabot.dnabot_app
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8 #if $adv.default_settings_file
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9 --default_settings_file '$adv.default_settings_file'
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10 #end if
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11 nogui
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12 --construct_path '$construct_file'
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13 #set files = '" "'.join([str($file) for $file in $plate_files])
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14 --source_paths "${files}"
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15 --etoh_well '$adv.etoh_well'
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16 --soc_column '$adv.soc_column'
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17 --output_dir 'output'
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18 && tar -cvf '$dnabot_scripts' 'output'
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19 ]]></command>
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20 <inputs>
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21 <param name="construct_file" type="data" format="csv" label="Source Construct" />
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22 <param name="plate_files" type="data" format="csv" multiple="true" label="Plate files" />
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23 <section name="adv" title="Advanced Options" expanded="false">
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24 <param name="default_settings_file" type="data" format="yaml" optional="true" label="Yaml file providing labware IDs and parameter to be used" />
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25 <param name="etoh_well" type="select" label="Well coordinate for Ethanol">
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26 <option value="A2" >A2</option>
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27 <option value="A3" >A3</option>
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28 <option value="A4" >A4</option>
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29 <option value="A5" >A5</option>
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30 <option value="A6" >A6</option>
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31 <option value="A7" >A7</option>
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32 <option value="A8" >A8</option>
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33 <option value="A9" >A9</option>
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34 <option value="A10" >A10</option>
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35 <option value="A11" selected="true">A11</option>
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36 </param>
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37 <param name="soc_column" type="select" label="Column coordinate for SOC">
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38 <option value="1" selected="true">1</option>
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39 <option value="2" >2</option>
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40 <option value="3" >3</option>
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41 <option value="4" >4</option>
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42 <option value="5" >5</option>
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43 <option value="6" >6</option>
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44 <option value="7" >7</option>
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45 <option value="8" >8</option>
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46 <option value="9" >9</option>
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47 <option value="10" >10</option>
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48 <option value="11" >11</option>
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49 <option value="12" >12</option>
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50 </param>
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51 </section>
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52 </inputs>
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53 <outputs>
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54 <data name="dnabot_scripts" format="tar" label="${tool.name} scripts" />
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55 </outputs>
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56 <tests>
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57 <test>
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58 <!-- test 1: check if identical outputs are produced with compress option -->
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59 <param name="construct_file" value="constructs.csv" />
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60 <param name="plate_files" value="user_parts_coords.csv,linker_parts_coords.csv"/>
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61 <output name="dnabot_scripts" file="dnabot_scripts.tar" compare="sim_size" decompress="True"/>
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62 </test>
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63 </tests>
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64 <help><![CDATA[
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65 DNA-Bot
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66 ============
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67
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68 DNA assembly using BASIC on OpenTrons
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69
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70 Input
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71 -----
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72
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73 * **default_settings_file**: (string) file providing labware IDs and parameter to be used. Default: dnabot/default_settings.yaml.
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74 * **construct_path**: (string) Construct CSV file.
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75 * **source_paths**: (string) Source CSV files.
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76 * **etoh_well**: (string) Well coordinate for Ethanol. Default: A11.
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77 * **soc_column**: (integer) Column coordinate for SOC. Default: 1.
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78 * **template_dir**: (string) Template directory. Default: "template_ot2_scripts" located next to the present script.
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79
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80 Ouput
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81 -----
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82
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83 * **output_dir**: (string) Output directory. Default: same directory than the one containing the "construct_path" file.
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84
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85 Version
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86 -------
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87
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88 3.0.0
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89
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90 Authors
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91 -------
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92
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93 * **Matthew C Haines**
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94 * Thomas Duigou
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95
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96 License
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97 -------
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98
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99 `MIT <https://github.com/brsynth/DNA-BOT/blob/DNA-BOT-APIv2/LICENSE>`_
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100
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101
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102 Acknowledgments
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103 ---------------
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104
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105 * Marko Storch
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106 * Geoff Baldwin
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107 ]]></help>
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108 <citations>
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109 <citation type="bibtex">
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110 @article{10.1093/synbio/ysaa010,
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111 author = {Storch, Marko and Haines, Matthew C and Baldwin, Geoff S},
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112 title = {DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology},
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113 journal = {Synthetic Biology},
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114 volume = {5},
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115 number = {1},
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116 year = {2020},
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117 month = {07},
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118 issn = {2397-7000},
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119 doi = {10.1093/synbio/ysaa010},
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120 url = {https://doi.org/10.1093/synbio/ysaa010},
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121 note = {ysaa010},
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122 eprint = {https://academic.oup.com/synbio/article-pdf/5/1/ysaa010/33722340/ysaa010.pdf},
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123 }
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124 </citation>
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125 </citations>
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126 </tool>